Transport secretary Philip Hammond confirmed the project would still go-ahead but the timetable will shift.
The announcement was part of a £14bn rail funding package unveiled today.
He said: “Over the next four years, we will provide £14 billion of funding to Network Rail to support capital maintenance and infrastructure investment; and £750 million for high speed rail.
“We will also fund the Crossrail project, the Tube upgrade programme, light rail projects in Birmingham, Tyneside, Nottingham and Sheffield; and provide additional funding to franchisees for extra rolling stock.
“Today, I can confirm we will fund and deliver the Thameslink programme in its entirety.
“But the original programme for the rebuilding of London Bridge was always ambitious, with substantial risks around delivery, and operation of existing services, during construction.
To reduce these risks, we have re-profiled the delivery of the programme to achieve completion in 2018. This will enable Network Rail to make further efficiencies to their design and delivery programme.
“As a first step, Network Rail will electrify the commuter services on the Great Western Main Line from London to Didcot, Oxford and Newbury over the next six years.
“ Network Rail will also electrify the lines between Liverpool, Manchester, Preston and Blackpool – an investment of up to £300 million. Work is expected to begin next year and to be finished in 2016. As with Thameslink, we expect Network Rail to keep a tight rein on costs.”